Evidence for two concurrent mechanisms and a kinetically significant proton transfer process in acid-catalyzed O-methyloxime formation

Stepwise versus Concerted: Theoretical Insights into the Stereoselectivity in Aryl Imine Formation Assisted by Acid and Water

The wide applications of the aryl Schiff base require extensive understanding of the mechanism of its formation, which remains unclear. In this work, the detailed formation mechanisms between benzaldehyde and aniline or 4-(9-anthryl) ethynyl aniline were investigated at the CCSD(T)//B3LYP level, and the influence of water molecules and acid catalysis and the stereoselectivity were addressed. The results show that the participation of explicit water molecules greatly accelerates the reactions by alleviating the ring tension of the transition states, and acid catalysis strongly favors the imine formation and provides driving force for the forward reaction. In acidic conditions, both N-protonated carbinolamine formations and imine formations are achieved under mild conditions with the assistance of water molecules, and the proton transfer is more advanced than the C-N and C═N bond formation, which is in good agreement with the experimental observations. In contrast, under neutral conditions, even with the assistance of two water molecules, the reaction is hard to take place at room temperature owing to the high Gibbs free energy barriers with the proton transfer and the C-N or C═N bond formation concerted. The analysis of stereoselectivity shows that the formation of trans imine is both kinetically and thermodynamically more favorable than the cis one under the acidic condition with the assistance of water molecules, and the presence of conjugated substituent 4-(9-anthryl) ethynyl of aniline marginally raises the energy barriers. This work provides a systematic view of the mechanism for the formation of aryl imine and is expected to offer insights for the control of the dynamic covalent chemistry and the synthesis of covalent organic frameworks.

Chemoenzymatic one-pot reaction from carboxylic acid to nitrile via oxime

We report a new chemoenzymatic cascade starting with aldehyde synthesis by carboxylic acid reductase (CAR) followed by chemical in situ oxime formation. The final step to the nitrile is catalyzed by aldoxime dehydratase (Oxd). Full conversions of phenylacetic acid and hexanoic acid were achieved in a two-phase mode.

We report a new chemoenzymatic cascade starting with aldehyde synthesis by carboxylic acid reductase (CAR) followed by chemical in situ oxime formation and enzymatic dehydration by aldoxime dehydratase (Oxd).

Eco-friendly methoximation of aromatic aldehydes and ketones using MnCl2.4H2O as an easily accessible and efficient catalyst

Methoximes are important as a class of intermediates and products, among fine chemicals and specialties. The development of a new, facile and efficient method for their synthesis is reported. The methoximes were properly accessed from the corresponding aromatic aldehydes and ketones in good to excellent yields, under mild conditions, employing the inexpensive and environmentally friendly MnCl2.4H2O as a catalyst (at low loading and without the addition of ligand), in EtOH at 50°C. The scope of the process was systematically assessed.

Complexes of Formaldehyde and α-Dicarbonyls with Hydroxylamine: FTIR Matrix Isolation and Theoretical Study

The interactions of formaldehyde (FA), glyoxal (Gly) and methylglyoxal (MGly) with hydroxylamine (HA) isolated in solid argon and nitrogen were studied using FTIR spectroscopy and ab initio methods. The spectra analysis indicates the formation of two types of hydrogen-bonded complexes between carbonyl and hydroxylamine in the studied matrices. The cyclic planar complexes are stabilized by O–H⋯O(C), and C–H⋯N interactions and the nonplanar complexes are stabilized by O–H⋯O(C) bond. Formaldehyde was found to form with hydroxylamine, the cyclic planar complex and methylglyoxal, the nonplanar one in both argon and nitrogen matrices. In turn, glyoxal forms with hydroxylamine the most stable nonplanar complex in solid argon, whereas in solid nitrogen, both types of the complex are formed.

New Polyaminoisoprenyl Antibiotics Enhancers against Two Multidrug-Resistant Gram-Negative Bacteria from Enterobacter and Salmonella Species

A series consisting of new polyaminoisoprenyl derivatives were prepared in moderate to good chemical yields varying from 32 to 64% according to two synthetic pathways: (1) using a titanium-reductive amination reaction affording a 50/50 mixture of cis and trans isomers and (2) a direct nucleophilic substitution leading to a stereoselective synthesis of the compounds of interest. These compounds were then successfully evaluated for their in vitro antibiotic enhancer properties against resistant Gram-negative bacteria of four antibiotics belonging to four different families. The mechanism of action against Enterobacter aerogenes of one of the most efficient of these chemosensitizing agents was precisely evaluated by using fluorescent dyes to measure outer-membrane permeability and to determine membrane depolarization. The weak cytotoxicity encountered led us to perform an in vivo experiment dealing with the treatment of mice infected with Salmonella typhimurium and affording preliminary promising results in terms of tolerance and efficiency of the polyaminoisoprenyl derivative 5r/doxycycline combination.

Hydrolytic Decomposition of S-Aroylthiooximes: Effect of pH and N-Arylidene Substitution on Reaction Rate

The hydrolytic decomposition of four peptides containing S-aroylthiooximes (SATOs) with variable N-arylidene substituents was investigated in 10 aqueous buffer solutions at pH values ranging from 6.0 to 10.9. UV-vis spectroscopy was employed to study the reaction kinetics, which revealed V-shaped pH-rate profiles for all peptides with a minimum near pH 8, suggesting a change from an acid-catalyzed to a base-activated reaction. Hammett plots showed positive ρ values above pH 8 and negative ρ values below pH 8, providing further evidence for a mechanism change. Based on these data, along with mass spectral evidence, we propose specific acid catalysis under mildly acidic and neutral conditions and multiple base-promoted decomposition reactions under mildly basic conditions.

Investigating Glyoxylate-Mediated Transamination Using Dipeptide Arrays and Proteomic Peptide Mixtures

Glyoxylate-mediated transamination (GT) is a classic, potentially general, and N-terminus-specific protein modification method useful for the preparation of bioconjugates. However, there is a lack of information on whether and how readily a particular N-terminal amino acid (in the context of a peptide chain) can be converted to the 2-oxoacyl moiety under GT conditions. Here, we conducted a systematic investigation of GT using membrane-bound dipeptide arrays that include all the 400 possible dipeptide combinations of the 20 genetically encoded amino acids. This colorimetric method offers a convenient way to assess the GT reaction tendency of N-terminal residues by the naked eye. It also provides interesting information about the effect of the second residues on GT, which has not been reported previously. In addition, we also designed a proteomics approach to study GT in solution using tryptic peptide mixtures, which not only confirmed many of our findings in peptide array assays but also revealed potential side reaction products. Taken together, our studies will make the future use of GT for protein modification in a much more predictable way.

The Importance of the MM Environment and the Selection of the QM Method in QM/MM Calculations: Applications to Enzymatic Reactions

In this chapter, we discuss the influence of an anisotropic protein environment on the reaction mechanisms of saccharopine reductase and uroporphyrinogen decarboxylase, respectively, via the use of a quantum mechanical and molecular mechanical (QM/MM) approach. In addition, we discuss the importance of selecting a suitable DFT functional to be used in a QM/MM study of a key intermediate in the mechanism of 8R-lipoxygenase, a nonheme iron enzyme. In the case of saccharopine reductase, while the enzyme utilizes a substrate-assisted catalytic pathway, it was found that only through treating the polarizing effect of the active site, via the use of an electronic embedding formalism, was agreement with experimental kinetic data obtained. Similarly, in the case of uroporphyrinogen decarboxylase, the effect of the protein environment on the catalytic mechanism was found to be such that the calculated rate-limiting barrier is in good agreement with related experimentally determined values for the first decarboxylation of the substrate. For 8R-lipoxygenase, it was found that the geometries and energies of the multicentered open-shell intermediate complexes formed during the mechanism are quite sensitive to the choice of the density functional theory method. Thus, while density functional theory has become the method of choice in QM/MM studies, care must be taken in the selection of a particular high-level method.

Mechanisms of imine exchange reactions in organic solvents

The state of the art in the mechanisms operating in imine chemistry in organic solvents is critically discussed in the present review. In particular, the reaction pathways involved in imine formation, transimination and imine metathesis in organic media are taken into account, with the aim of organizing the poor, and sometimes scattered, information available in the literature. It is shown that 4-membered cyclic transition states, either polar or apolar, can be considered a leitmotif for the chemistry of imines in organic solvents. However, it is pointed out that further investigations will be necessary to reach an adequate degree of knowledge of the mechanisms involved in such important reversible processes.

Reactivity of a phospholipid monolayer model under periodic boundary conditions: a density functional theory study of the Schiff base formation between phosphatidylethanolamine and acetaldehyde

A mechanism for the formation of the Schiff base between an acetaldehyde and an amine-phospholipid monolayer model based on Dmol3/density functional theory calculations under periodic boundary conditions was constructed. This is the first time such a system has been modeled to examine its chemical reactivity at this computation level. Each unit cell contains two phospholipid molecules, one acetaldehyde molecule, and nine water molecules. One of the amine-phospholipid molecules in the cell possesses a neutral amino group that is used to model the nucleophilic attack on the carboxyl group of acetaldehyde, whereas the other has a charged amino group acting as a proton donor. The nine water molecules form a hydrogen bond network along the polar heads of the phospholipids that facilitates very fast proton conduction at the interface. Using periodic boundary conditions afforded proton transfer between different cells. The reaction takes place in two steps, namely, (1) formation of a carbinolamine and (2) its dehydration to the Schiff base. The carbinolamine is the primary reaction intermediate, and dehydration is the rate-determining step of the process, consistent with available experimental evidence for similar reactions. On the basis of the results, the cell membrane surface environment may boost phospholipid glycation via a neighboring catalyst effect.

Glycosylation of aromatic amines II: Kinetics and mechanisms of the hydrolytic reaction between kynurenine and glucose

The kinetics of the weakly basic aromatic amine, kynurenine, with glucose were studied as model reactants aimed at mechanistic understanding of pharmaceutically relevant amine-aldehyde reactions. The reaction kinetics of the forward and reverse processes (glycosylamine formation and hydrolysis) were studied under first-order conditions in aqueous solutions at 40 degrees C in the pH range 1-6.5 in the presence of various buffers. The alpha-and beta-glycosylamines were reversibly formed via an acyclic imine that was not present in detectable quantities. Rate-limiting formation of the imine was complex and involved the addition of the amine and aldehyde to form the carbinolamine followed by the acid-catalyzed dehydration to the imine. The pH-rate profile was characterized by three kinetically distinguishable processes. At lower pH values, the profile was consistent with specific acid-catalyzed rate-determining addition of amine and aldehyde. In the pH range of 4-6 a downward bend was attributable to the change in rate determining step from addition to dehydration. In the pH region of 2-3 the rate law was described by specific acid catalysis and solvolysis of the zwitterionic form of kynurenine. Nonlinear buffer effects and Brönsted plots were shown to be consistent with this interpretation of the pH-rate profile.

Optimization of a biomimetic transamination reaction

For a range of protein substrates, N-terminal transamination offers a convenient way to install a reactive ketone or aldehyde functional group at a single location. We report herein the effects of the identity of N-terminal residues on the product distribution generated upon reaction with pyridoxal 5'-phosphate (PLP). This study was accomplished through the combination of solid-phase peptide synthesis with detailed liquid chromatography-mass spectrometry analysis. Many N-terminal amino acids provided high yields of the desired transaminated products, but some residues (His, Trp, Lys, and Pro) generated adducts with PLP itself. N-terminal Cys and Ser residues were observed to undergo beta-elimination in addition to transamination, and the transamination product of N-terminal Gln was resistant to subsequent oxime formation attempts. The information generated through the screening of peptide substrates was successfully applied to a protein target, changing an initially unreactive terminus into one that could be modified in high (70%) yield. Thus, these studies have increased our predictive power for the reaction, both in terms of improving conversion and suppressing reaction byproducts. An initial set of guidelines that may be used to increase the applicability of this reaction to specific proteins of interest is provided.

Insights on co-catalyst-promoted enamine formation between dimethylamine and propanal through ab initio and density functional theory study

The mechanistic details on enamine formation between dimethylamine and propanal are unraveled using the ab initio and density functional theory methods. The addition of secondary amine to the electrophile and simultaneous proton transfer results in a carbinolamine intermediate, which subsequently undergoes dehydration to form enamine. The direct addition of amine as well as the dehydration of the resulting carbinolamine intermediate is predicted to possess fairly high activation barrier implying that a unimolecular process is unlikely to be responsible for enamine formation. Different models are therefore proposed which could explain the relative ease of enamine formation under neat condition as well as under the influence of methanol as the co-catalyst. The explicit inclusion of either the reagent or the co-catalyst is considered in the transition states as stabilizing agents. The participation of the reagent or the co-catalyst as a monofunctional ancillary species is found to stabilize the transition states relative to the unassisted or the direct addition/dehydration pathways. The reduction in enthalpy of activation is found to be much more dramatic when two co-catalysts participate in an active bifunctional mode in the rate-determining dehydration step. The transition structures exhibited characteristic features of a relay proton transfer mechanism. The free energy of activation associated with the two methanol-assisted pathway is found to be 16.7 kcal/mol lower than that of the unassisted pathway. The results are found to be in concurrence with the available reports on the rate acceleration by co-catalysts in the Michael reaction between enamine and methyl vinyl ketone under neat conditions.

Chemical Characterization of α-Oxohydrazone Ligation on Colloids: toward Grafting Molecular Addresses onto Biological Vectors

New mild and specific chemical strategies have been developed recently for the selective coupling of biological macromolecules. Among them, the hydrazone ligation strategy offers high chemoselectivity and versatility. We intended to use hydrazone ligation to target the controlled release of therapeutic agents by biological vectors (multilamellar vesicles called onion vectors). An accurate measure of ligation bond stability was needed to ensure that the ligation bond would stand long exposures to physiological conditions. In this study, we have completed a kinetic and thermodynamic characterization of hydrazone formation on a model reaction. The mechanism of the reaction in solution as well as in different self-organized systems (micelles, liposomes and multilamellar vesicles) was investigated. In solution, submicromolar stability was achieved as well as half-lives of several weeks. The kinetics and stability were both enhanced in colloidal media thanks to autoassociation effects. The results were expanded to the realistic case of RGD-peptide coupling to onion vectors. The RGD grafted onion vectors were then tested for their ability to bind endothelial cells in vitro.